HDF5 version 1.8.2-post10 currently under development ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.2 and HDF5 1.8.2-snap*, and contains information on the platforms tested and known problems in HDF5-1.8.2-snap*. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.2 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.2 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.2 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, including brief general descriptions of some new and modified APIs, are described in the "What's New in 1.8.0?" document: http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.8.2 (current release) versus Release 1.8.1": http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - Support for new platforms and languages - Bug Fixes since HDF5-1.8.2 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Add description here. Do not exceed 80 characters per line. EIP - 2008/11/12 Library ------- - Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29 - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a user-defined callback function for external link traversal. NAF - 2009/01/08 - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to allow the user to specify the file access flags used to open the target file of an external link. NAF - 2009/01/08 - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow individual rdcc configuration for each dataset. Added H5Dget_access_plist() function to retrieve a dataset access property list from a dataset. NAF - 2008/11/12 - Added H5Iis_valid() function to check if an id is valid without producing an error message. NAF - 2008/11/5 - Added code to maintain a min_clean_fraction in the metadata cache when in serial mode. MAM - 2009/01/9 Parallel Library ---------------- Tools ----- - h5repack now handles group creation order. PVN - 2009/4/2 - 1402 - h5repack: When user doesn't specify a chunk size, h5repack now defines a default chunk size as the same size of the size of the hyperslab used to read the chunks. The size of the hyperslabs are defined as the size of each dimension or a predefined constant, whatever is smaller. This assures that the chunk read fits in the chunk cache. PVN - 2008/11/21 High-Level APIs: ------ - Table: In version 3.0 of Table, the writing of the "NROWS" attribute (used to store number of records)was deprecated. PVN - 2008/11/24 Fortran High-Level APIs: ------ - Lite: The h5ltget_dataset_info_f function (gets information about a dataset) was not correctly returning the dimension array (PVN - 2009/3/23) F90 API ------ C++ API ------ Support for New Platforms, Languages, and Compilers =================================================== Bug Fixes since HDF5-1.8.2 ========================== Configuration ------------- - The --includedir=DIR configuration option now works as intended, and can be used to specify the location to install C header files. The default location remains unchanged, residing at ${prefix}/include. MAM - 2009/03/10 - BZ #1381 - Configure no longer removes the '-g' flag from CFLAGS when in production mode if it has been explicitly set in the CFLAGS environment variable prior to configuration. MAM - 2009/03/09 - BZ #1401 Library ------- - Fixed a bug that caused files with a user block to grow by the size of the user block every time they were opened. NAF - 2009/03/26 - 1499 - Fixed a rare problem that could occur with files using the old (pre 1.4) array datatype. NAF - 2009/03/23 - Modified library to be able to open files with corrupt root group symbol table messages, and correct these errors if they are found. Such files can only be successfully opened with write access. NAF - 2009/03/23 - 1189 - Removed the long_long #define and replaced all instances with "long long". This caused problems with third party products. All currently supported compliers support the type. (ADB - 2009/03/05) - Fixed various bugs that could prevent the fill value from being written in certain rare cases. NAF - 2009/02/26 - 1469 - Fixed a bug that prevented more than one dataset chunk from being cached at a time. NAF - 2009/02/12 - 1015 - Fixed an assertion failure caused by opening an attribute multiple times through multiple file handles. NAF - 2009/02/12 - 1420 - Fixed a problem that could prevent the user from adding attributes (or any object header message) in some circumstances. NAF - 2009/02/12 - 1427 - Fixed a bug that could cause problems when an attribute was added to a committed datatype using the committed datatype's datatype. NAF - 2009/02/12 - Fixed a bug that could cause problems when copying an object with a shared message in its own object header. NAF - 2009/01/29 - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes. NAF - 2009/01/27 - 1443 - Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise packed compound type. NAF - 2009/01/14 - Fixed up some old v2 btree assertions that get run in debug mode that were previously failing on compilation, and removed some of the more heavily outdated and non-rewritable ones. MAM - 2008/12/15 - Fixed a bug that could cause problems when "automatically" unmounting multiple files. NAF - 2008/11/17 - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. PVN - 2009/01/8 Parallel Library ---------------- Tools ----- - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets that have a datatype datum size greater than H5TOOLS_BUFSIZE, a constant defined as 1024Kb, such as array types with large dimensions. PVN - 2009/4/1 - 1501 - h5import: By selecting a compression type, a big endian byte order was being selected. PVN - 2009/3/11 - 1462 - zip_perf.c had missing argument on one of the open() calls. Fixed. AKC - 2008/12/9 F90 API ------ C++ API ------ Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 7.0.0.8 xlf 09.01.0000.0008 xlC 7.0.0.8 mpcc_r 7.0.0.8 mpxlf_r 09.01.0000.0008 Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.5 20080702 g++ 4.2.5 20080702 gfortran 4.2.5 20080702 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.5 20080702 g++ 4.2.5 20080702 gfortran 4.2.5 20080702 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 SMP i686 i386 G95 (GCC 4.0.3 (g95 0.92!) April 18 2007) (kagiso) PGI C, Fortran, C++ 7.2-1 32-bit Intel(R) C Compiler for 32-bit applications, Version 10.1 Intel(R) C++ Compiler for 32-bit applications, Version 10.1 Intel(R) Fortran Compiler for 32-bit applications, Version 10.1 Absoft 32-bit Fortran 95 10.0.4 MPICH mpich-1.2.7 compiled with gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.6p1 compiled with gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T SMP x86_64 GNU/Linux Ver. 10.1.013 (smirom) Intel(R) Fortran Intel(R) EM64T Ver. 10.1.013 PGI C, Fortran, C++ Version 7.2-1 for 64-bit target on x86-64 MPICH mpich-1.2.7 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.7 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) tested for both 32- and 64-bit binaries Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 (cobalt) SGI MPI 1.16 SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8 (linew) Sun WorkShop 6 update 2 Fortran 95 8.2 Sun WorkShop 6 update 2 C++ 5.8 Patch 121019-06 Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) Intel(R) C++ Version 10.0.026 Intel(R) Fortran Compiler Version 10.0.026 Open MPI 1.2.2 MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 compiled with icc v10.0.026 and ifort 10.0.026 IA-64 Linux 2.4.21-309.tg1 #1 SMP ia64 gcc (GCC) 3.2.2 (NCSA tg-login) Intel(R) C++ Version 8.1.037 Intel(R) Fortran Compiler Version 8.1.033 mpich-gm-1.2.7p1..16-intel-8.1.037-r1 Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) gcc 3.4.6 20060404 Intel(R) C++ Version 10.0 Intel (R) Fortran Compiler Version 10.0 mvapich2-0.9.8p2patched-intel-ofed-1.2 Windows XP Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 MAC OS 10.5.4 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) Intel C, C++ and Fortran compilers 10.1 Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release x = not working in this release dna = does not apply ( ) = footnote appears below second table = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y IRIX64_6.5 32-bit n n n n y y IRIX64_6.5 64-bit n y y y y y Windows XP n y(15) n(15) y y y Windows XP x64 n y(15) n(15) y y y Windows Vista n n n y y y Mac OS X 10.5 Intel n y n y y y AIX 5.3 32- and 64-bit n y n y y n FreeBSD 6.3-STABLE 32&64 bit n y n y y y RedHat EL4 (3) W y(1) y(10) y(1) y y y RedHat EL4 Intel (3) W n y n y y n RedHat EL4 PGI (3) W n y n y y n SuSe x86_64 gcc(3,12) W y(2) y(11) y(2) y y y SuSe x86_64 Int(3,12) W n y(13) n y y n SuSe x86_64 PGI(3,12) W n y(8) n y y y Linux 2.6 SuSE ia64 C Intel (3,7) y y y y y n Linux 2.6 SGI Altix ia64 Intel (3) y y y y y y Linux 2.6 RHEL C Lustre Intel (5) y(4) y y(4) y y n Cray XT3 2.0.41 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y IRIX64_6.5 32-bit y dna y y IRIX64_6.5 64-bit y y n y Windows XP y y(15) y y Windows XP x64 y y(15) y y Windows Vista y n n y Mac OS X 10.5 y n y n AIX 5.3 32- and 64-bit n n n n FreeBSD 6.2 32&64 bit y n y y RedHat EL4 (3) W y y(10) y y RedHat EL4 Intel (3) W y y y n RedHat EL4 PGI (3) W y y y n SuSe x86_64 GNU(3,12) W y y y y SuSe x86_64 Int(3,12) W y y y n SuSe x86_64 PGI(3,12) W y y y n Linux 2.4 SuSE C ia64 C Intel (7) y y y n Linux 2.4 SGI Altix C ia64 Intel y n Linux 2.6 RHEL C Lustre Intel (5) y y y n Cray XT3 2.0.41 n n n n Notes: (1) Using mpich2 1.0.6. (2) Using mpich2 1.0.7. (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. (4) Using mvapich2 0.9.8. (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers (8) pgf90 (9) With Compaq Visual Fortran 6.6c compiler. (10) With PGI and Absoft compilers. (11) PGI and Intel compilers for both C and Fortran (12) AMD Opteron x86_64 (13) ifort (14) Yes with C and Fortran, but not with C++ (15) Using Visual Studio 2005 or Cygwin (16) Not tested for this release. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * We have discovered two problems when running collective IO parallel HDF5 tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a Linux cluster at NCSA. Under some complex selection cases: 1) MPI_Get_element returns the wrong value. 2) MPI_Type_struct also generates the wrong derived datatype and corrupt data may be generated. These issues arise only when turning on collective IO with chunking storage with some complex selections. We have not found these problems on other MPI-IO compilers. If you encounter these problems, you may use independent IO instead. To avoid this behavior, change the following line in your code H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); to H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); KY - 2007/08/24 * On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, use -mp -O1 compilation flags to build the libraries. A higher level of optimization causes failures in several HDF5 library tests. * For LLNL, uP: both serial and parallel tests pass. Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. ubgl: Serial tests pass but parallel tests fail. * On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and the application asks to do collective IO, we have found that when using 4 processors, a simple collective write will sometimes be hung. This can be verified with t_mpi test under testpar. * On IRIX6.5, when the C compiler version is greater than 7.4, complicated MPI derived datatype code will work. However, the user should increase the value of the MPI_TYPE_MAX environment variable to some appropriate value to use collective irregular selection code. For example, the current parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. SLU - 2005/6/30 * On IBM AIX systems, parallel HDF5 mode will fail some tests with error messages like "INFO: 0031-XXX ...". This is from the command `poe'. Set the environment variable MP_INFOLEVEL to 0 to minimize the messages and run the tests again. The tests may fail with messages like "The socket name is already in use", but HDF5 does not use sockets. This failure is due to problems with the poe command trying to set up the debug socket. To resolve this problem, check to see whether there are many old /tmp/s.pedb.* files staying around. These are sockets used by the poe command and left behind due to failed commands. First, ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. * The --enable-static-exec configure flag fails to compile for Solaris platforms. This is due to the fact that not all of the system libraries on Solaris are available in a static format. The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platforms for serial mode. The parallel mode works fine with this option. It is suggested that you do not use this option on these platforms during configuration. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * Information about building with PGI and Intel compilers is available in the INSTALL file sections 4.7 and 4.8.